I recently purchased an antibody to identify the protein I am studing by western blotting. The protein expression in the membrane revelation remains the same as in my control (cells without overexpression). However, when I mark it with an anti-flag, which is the tag that is linked to the protein sequence, the signal is much stronger. I already did the sequencing of my protein and everything is ok. Is it possible that the antibody does not recognize the flagged protein and only recognizes the endogenous protein?

The antibody recognizes a structured region of the protein and the flag tag is in the C-end.